Appendix A Genotypes and phenotypes of rice materials used

Appendix A Genotypes and phenotypes of rice materials used in this study.

Rice materials Genotype

Phenotype

Panicle Grain

Nipponbare qPE9-1 GS9 Drooping panicle Round grain

N138 line qPE9-1 gs9 Drooping panicle Longer and narrower grain

2661 qpe9-1 GS9 Erect panicle Round grain

NIL in 2661 qpe9-1 gs9 Erect panicle Longer and narrower grain

NIL in 2661 qPE9-1 GS9 Drooping panicle Round grain

NIL in 2661 qPE9-1 gs9 Drooping panicle Longer and narrower grain

WYJ27 qpe9-1 GS9 Erect panicle Round grain

IL in WYJ27 qpe9-1 GS9 Erect panicle Round grain

IL in WYJ27 qpe9-1 gs9 Erect panicle Longer and narrower grain

IL in WYJ27 qPE9-1 GS9 Drooping panicle Round grain

IL in WYJ27 qPE9-1 gs9 Drooping panicle Longer and narrower grain

Appendix B Primers used for genotype identification in this study.

Primer Sequence Physical position

IN0919 CGTTTAGGCTGGCTGC

16,748,418-16,748,610

CAGTTGGTGGTTTCGTAGAG

IN0911 GGCTGACACTCTGGAACTGGA

16,774,528-16,774,641

GCCTGGGCAGAGGGTGAG

IN0901 GTGCTTTGGAACCACTCT

16,413,327-16,413,472

ATAGCAAATGGCAAATGG

IN0902 GGCCCACTGGTCCAACAA

16,413,701-16,413,823

ATCGGTGAAACAAATCTCAGGAC

Appendix C Primers used for gene function analysis in this study.

Primer Sequence Function

RTGS9 GACGCAAGCAGCGACCAGCA Expression

analysis GCCTGGCAGTTGGAGGATGAGC

RTqPE9 GCTCAGCCCGTTTCTCGTT

GAGCACGAGCAGTTCGGTTT

RTGS3 CCGCGAGATCGGATTCC

CGTGGATCCCTTCGATTGA

RTGGC2 GTGCAACTGCTTGTTATGCC

GCTCGGTCTACAGCACGAT

RTRGA1 TGAGGCTGAAACAACCAAA

GCTCCTAAGTTCTGCCTCAT

RGRGB1 GCTGCCTTGGTCTTTCTTCT

GGCCCAAATCTTCAAATTCT

RTRGG1 GCTTGATAAAACGGATAAGGTGTC

GCGGACCTTCAAACCATCTGT

RTRGG2 GCGGAATCATCTGCGGGACG

TGGATGCCCACCATTTGTTACTGC

BDGS9 CATATGATGCAGAGCAGCAGCAAGCGGC Vector

construction GTCGACCATCGTCTTCGTCTTCGTCGTCA

ADOFP8 GAATTCCCAGTGGCATTGTCCATGTCG

GGATCCGGCGTCGCGTTGAAACTTGG

ADqPE9 GAATTCGGCGATTTATACCCACCACG

GGATCCCGAACTTAATCAAAGGCCTAACAACTA

ADGS3 CATATGTCTCCATTATCGGAACTTCGGAGTGA

GAGCTCCCAATCAGTGCAGCTTCGCTCAATC

Appendix D Comparison of transcript abundance for genes involved in the G protein pathway in young panicles between NPB-gs9 (gs9) and ‘Nipponbare’ (GS9).

Transcripts BaseMean_GS9 BaseMean_gs9 FoldChange p val Gene product

LOC_Os03g43480.1/RGG1 0.000 0.000 AGG2, putative, expressed

LOC_Os02g04520.1/RGG2 663.006 817.305 1.233 0.208 AGG2, putative, expressed

LOC_Os02g04520.2/RGG2 219.691 174.687 0.795 0.238

LOC_Os06g09930.1 972.191 936.463 0.963 0.669 G protein coupled receptor, putative, expressed

LOC_Os07g30300.1 1075.516 1203.555 1.119 0.276 small G protein family protein, putative, expressed

LOC_Os02g37570.1 0.000 0.697 keratin-associated protein 5-3, putative, expressed

LOC_Os09g26999.1/qPE9-1 1879.106 2158.374 1.149 0.064

keratin-associated protein 5-4, putative, expressed LOC_Os09g26999.2/qPE9-1 1615.991 2002.509 1.239 0.029

LOC_Os09g26999.3/qPE9-1 341.187 382.628 1.121 0.807

LOC_Os05g26890.1/RGA1 1545.919 1512.090 0.978 0.782 G-protein alpha subunit, putative, expressed

LOC_Os06g02130.1 3719.099 3668.063 0.986 0.892 G-protein alpha subunit, putative, expressed

LOC_Os06g02130.2 24.318 88.280 3.630 0.010


LOC_Os10g02814.2 95.730 97.733 1.021 0.825



LOC_Os01g43330.1 6294.474 6051.122 0.961 0.553 extra-large G-protein-related, putative, expressed


LOC_Os02g15820.2 22.542 1.758 0.078 0.004


LOC_Os05g50910.2 22.391 13.804 0.616 0.707


LOC_Os01g03510.1 4487.954 4191.982 0.934 0.292 WD domain, G-beta repeat domain containing protein, expressed









LOC_Os01g28680.1 67.616 12.010 0.178 0.011

WD domain, G-beta repeat domain containing protein, expressed

LOC_Os01g28680.2 12.846 13.537 1.054 1.000

LOC_Os01g28680.3 16.398 31.634 1.929 0.529

LOC_Os01g28680.4 9.706 49.702 5.121 0.006

LOC_Os01g28680.5 2.276 0.562 0.247 0.748

LOC_Os01g28680.7 40.886 23.684 0.579 0.330

LOC_Os01g28680.8 155.640 155.051 0.996 0.942

LOC_Os01g28680.9 20.259 29.844 1.473 0.556

LOC_Os01g28680.10 21.090 9.672 0.459 0.371

LOC_Os01g28680.12 48.602 56.293 1.158 0.730

LOC_Os01g28680.13 6.631 0.562 0.085 0.390





LOC_Os01g51300.2 10517.015 10011.762 0.952 0.364








LOC_Os02g04320.2 189.655 143.823 0.758 0.228




LOC_Os02g18820.2 1236.232 1087.747 0.880 0.296




LOC_Os02g32430.2 369.514 347.997 0.942 0.714

LOC_Os02g33630.1 0.000 0.986 WD domain, G-beta repeat domain containing protein, expressed



LOC_Os02g45810.2 0.000 2.120


LOC_Os02g49090.2 33.108 12.637 0.382 0.332




LOC_Os03g02110.2 330.713 292.773 0.885 0.454










LOC_Os03g46650.1/RGB1 5247.108 4929.878 0.940 0.339 WD domain, G-beta repeat domain containing protein, expressed



LOC_Os03g49200.2 0.865 8.648 9.998 0.162




LOC_Os03g54770.1 679.035 689.413 1.015 0.921

WD domain, G-beta repeat domain containing protein, expressed LOC_Os03g54770.2 0.000 0.000

LOC_Os03g54770.3 6.227 7.416 1.191 0.940



LOC_Os03g61630.2 52.802 49.474 0.937 0.907


LOC_Os04g11880.1 4665.262 4413.351 0.946 0.421

WD domain, G-beta repeat domain containing protein, expressed LOC_Os04g11880.2 321.422 203.403 0.633 0.342

LOC_Os04g11880.3 165.870 170.454 1.028 0.867







LOC_Os05g05210.2 21.192 14.531 0.686 0.705

LOC_Os05g16660.1 3171.068 2932.892 0.925 0.285


LOC_Os05g16660.3 45.266 43.708 0.966 0.992




LOC_Os05g44320.1 1891.450 1774.158 0.938 0.491


LOC_Os05g44320.3 330.988 400.034 1.209 0.400



LOC_Os06g04040.1 511.102 494.325 0.967 0.723


LOC_Os06g04040.3 99.957 202.434 2.025 0.006



LOC_Os06g19660.2 2790.124 2426.674 0.870 0.092




LOC_Os06g44030.2 3912.352 3846.810 0.983 0.708









LOC_Os07g22534.1 92.781 80.488 0.868 0.647


LOC_Os07g22534.3 188.205 160.931 0.855 0.442

LOC_Os07g22534.4 106.287 121.030 1.139 0.731


LOC_Os07g25440.2 66.777 65.230 0.977 0.959


LOC_Os07g32350.2 388.625 390.519 1.005 0.897


LOC_Os07g40030.1 2198.435 2172.524 0.988 0.921


LOC_Os07g40030.3 38.210 45.741 1.197 0.919




LOC_Os08g04270.1 2316.554 2130.170 0.920 0.374


LOC_Os08g04270.3 108.648 120.355 1.108 0.792

LOC_Os08g04290.1 0.000 0.000 WD domain, G-beta repeat domain containing protein, expressed




LOC_Os08g21660.2 69.324 41.958 0.605 0.294


LOC_Os08g44010.1 30.200 17.312 0.573 0.254

WD domain, G-beta repeat domain containing protein, expressed

LOC_Os08g44010.2 523.440 481.747 0.920 0.562

LOC_Os08g44010.3 1585.622 1519.612 0.958 0.615

LOC_Os08g44010.4 233.930 240.324 1.027 0.753

LOC_Os08g44010.5 222.255 245.825 1.106 0.677




LOC_Os09g09470.2 120.861 100.146 0.829 0.610








LOC_Os10g32710.1 2366.506 2310.134 0.976 0.731


LOC_Os10g32710.3 322.387 363.227 1.127 0.506










LOC_Os12g03822.2 10.816 26.802 2.478 0.416

LOC_Os12g06810.1 4266.262 4073.663 0.955 0.464


LOC_Os12g06810.3 102.489 71.958 0.702 0.184

LOC_Os12g06810.4 135.573 111.013 0.819 0.440

LOC_Os12g07450.1 3870.123 3884.393 1.004 0.962


LOC_Os12g07450.3 91.817 72.235 0.787 0.340

LOC_Os12g19590.1 1065.227 1052.476 0.988 0.861


LOC_Os12g19590.3 38.180 46.276 1.212 0.545


Appendix E Relative transcription of RGA1 (a), RGB1 (b), RGG1 (c), RGG2 (d), GS3 (e), and

GGC2 (f) in inflorescence that differ with respect to the GS9 alleles (wild-type or null gs9). Data

are given as means ± SD (n=3). NS indicates no significant difference (P <0.05, t-test).

Appendix F Analyses of interaction between GS9 and G protein subunits in yeast two-hybrid

assays. OsOFP8/LOC_Os01g64430 protein was selected as the positive control. The G protein

subunit genes used were qPE9-1/Os09g0441900, RGA1/Os05g0333200, RGB1/Os03g0669200,

RGG1/Os03g0635100, RGG2/Os02g0137800, GS3/Os03g0407400, and GGC2/Os08g0456600.

Appendix G Plant height and panicle length of plants grown in Hainan field. a, Plant height of

2661 and three NILs. b, Panicle length of 2661 and three NILs. 2661(GS9/qpe9-1), wild type 2661;

NIL(gs9/qpe9-1), NIL carrying the gs9 and qpe9-1 alleles; NIL(GS9/qPE9-1), NIL carrying the

GS9 and qPE9-1 alleles; NIL(gs9/qPE9-1), NIL carrying the gs9 and qPE9-1 alleles. c, Plant

height of ILs in WYJ27 background. d, Panicle lengths of ILs in WYJ27 background. Four ILs in

WYJ27 background were selected from the same segregating population. IL(GS9/qpe9-1), IL

carrying the GS9 and qpe9-1 alleles; IL(gs9/qpe9-1), IL carrying the gs9 and qpe9-1 alleles;

IL(GS9/qPE9-1), IL carrying the GS9 and qPE9-1 alleles; IL(gs9/qPE9-1), IL carrying the gs9 and

qPE9-1 alleles. Data are given as means ± SD (n=3). Different letters denote significant

differences (P <0.05, one-way ANOVA).

Appendix H Plant and panicle architecture of ILs in WYJ27 background grown in Yangzhou field.

a, Comparison of plant architecture in the ILs carrying different combinations of alleles of GS9

and qPE9-1 genes. Scar bar = 10 cm. b, Comparison of panicle architecture in the ILs. Scar bar =

1 cm. c-e, Plant height, panicle length, and panicle curvature in the ILs. Data are given as means ±

SD (n=5). Different letters denote significant differences (P <0.05, one-way ANOVA).

Appendix I Grain shape parameters in 2661 and three NILs grown in Hainan field. Grain length

(a), grain width (b), and grain length-width ratio (c) of 2661 and three NILs carrying different

combinations of GS9 and qPE9-1. Data are given as means ± SD (n=3). The different lowercase

letters indicate significant differences between the means (P <0.05, one-way ANOVA).

Appendix J Differences in grain shape and grain quality between ILs harboring the GS9 and gs9

alleles in WYJ27 background. The two ILs with erect panicles were homozygous for either GS9 or

gs9 allele. Grain length (a), grain width (b), and the grain length-width ratio (c) in Hainan field.

Additionally, apparent amylose content (d), viscosity (e), palatability value (f) in Yangzhou field.

Data are given as means ± SD (n=3). NS and * denote non-significant and significant differences

between the means (P <0.05, t-test), respectively.

Documents

Appendix A Genotypes and phenotypes of rice materials used